An unusual mixture of sketch comedy and oddball storytelling, the three Goons developed a roster of rather bizarre continuing characters, who each week would engage in surreal adventures across time, space, literature, and sanity.

Secombe played the protagonist, the dim Ned Seagoon, and occasional minor parts, while Sellers and Milligan between them populated the rest of their audio world. Sellers played the villainous Hercules Grytpype-Thynne, cowardly army man Major Bloodnok, cheeky child Bluebottle, decrepit old Henry Crun, Willium "Mate" Cobblers, and showbiz agent Lew (modeled after Lew Grade), among others, while Milligan played "The Famous Eccles," Grytype-Thynne's associate Count Jim Moriarty, Henry's spinster companion Minnie Banister, Little Jim, and more.

These odd characters were complemented by an even odder range of running jokes and catchphrases, from Little Jim's "He's fallen in the waa-ater" and Henry Crun's "You can't get the wood" to the nonsensical "Needle nardle noo!" (most often spoken by Seagoon). The offbeat characters, surreal happenings, music hall variety elements, and "show within a show" aspect later had a pronounced influence on The Muppet Show, which featured both Milligan and Sellers as guests.

In issue #3 of the 2009 The Muppet Show Comic Book: The Treasure of Peg-Leg Wilson, a group of dwarfs ask their expert, Topaz, for his opinion of Miss Piggy's jewels. He responds with a poem in the style of William J. McGoonagall, a character from The Goon Show who recites terrible doggerel in a portentous, dramatic manner. McGoonagall, a Milligan character (sometimes played by Sellers) began his recitations with a drawn-out "Oooooohhhhh...", before launching into rhyming couplets that broke the typical conventions of rhythm and good sense. McGoonagall was a spoof of a famously bad Scottish poet, William Topaz McGonagall, whose 1879 poem The Tay Bridge Disaster reminded the world that "the stronger we our houses build / the less chance we have of being killed." The closing lines of Topaz's poem are worthy of McGoonagall, or even McGonagall himself -- "Let us no more allow ourselves to be distracted / By gaudy baubles worn upon a pig whose roles are without exception terribly acted."

Issue #2 of the 2010 comic book story arc The Muppet Show Comic Book: On the Road also includes a Goon Show reference. Trying to frighten away insult comedian Clint Wacky, the rats stand nearby and whisper, "Apparently Kermit's got amphibian lurgi. Highly contagious!" The dreaded lurgi, a terrible but unspecified malady, was introduced in the 1954 Goon Show episode "Lurgi Strikes Britain." Villains Grytpype and Moriarty invent the imaginary disease to convince Seagoon (and the nation) to invest in the only known cure for lurgi -- brass band instruments, which Grytpype and Moriarty happen to manufacture. The word "lurgi" became a regular catchphrase on the show, and later entered the British dialect as a way to describe a vague feeling of being sick. While the slang word is now commonly spelled "lurgy," the comic book uses the original Goon Show spelling.

In issue #2 of the 2010 comic book Muppet Sherlock Holmes, Sherlock, Dr. Watson and Inspector Lestrade (played by Gonzo, Fozzie Bear and Kermit the Frog) create a series of distractions to fool Irene Adler (Miss Piggy) into revealing her secret hiding places. In one panel, Lestrade is struck down, and Holmes cries, "Oh no! The dreaded Batter Pudding Hurler of Bexhill on Sea has struck again!" This is a reference to a 1954 Goon Show episode, "The Dreaded Batter Pudding Hurler (of Bexhill-on-Sea)". Holmes' instruction to "search everyone for a small oven" echoes the Goons' story; the villain carried around an oven to keep his batter puddings warm.